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A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes
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Document Title
A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes
Author
Uengwetwanit T.,Pootakham W.,Nookaew I.,Sonthirod C.,Angthong P.,Sittikankaew K.,Rungrassamee W.,Arayamethakorn S.,Wongsurawat T.,Jenjaroenpun P.,Sangsrakru D.,Leelatanawit R.,Khudet J.,Koehorst J.J.,Schaap P.J.,Martins dos Santos V.,Tangy F.,Karoonuthaisiri N.
Name from Authors Collection
Scopus Author ID
56030033100
Affiliations
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand; National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand; Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States; Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand; Shrimp Genetic Improvement Center, Integrative Aquaculture Biotechnology Research Group, Surat Thani, Thailand; Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Wageningen, Netherlands; Viral Genomics and Vaccination Unit, UMR3569 CNRS, Virology Department, Institut Pasteur, Paris, France
Type
Article
Source Title
Molecular Ecology Resources
ISSN
1755098X
Year
2021
Volume
21
Issue
5
Page
1620-1640
Open Access
All Open Access, Hybrid Gold, Green
Publisher
Blackwell Publishing Ltd
DOI
10.1111/1755-0998.13357
Abstract
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming. © 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
Keyword
black tiger shrimp | growth-associated genes | Hi-C | PacBio | Penaeus monodon | reference genome | Transcriptomics
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
License
CC BY-NC-ND
Rights
Author
Publication Source
Scopus